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I am new to this area. I am a researcher working on fast pattern searching in general scenarios (e.g., regex in string matching).

I am curious about the "regular expression (regex)" (pattern/motif) in bioinformatics. Can anyone help point out some repository where I can see some "regex" instances (used by people in real cases)?

So that I can get a sense how complex they are and the possibility to apply our techniques.

Thank you!

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  • $\begingroup$ There are only a fixed types of characters for DNA or protein sequence. For inexact matches you can use a regex. People do it quite often for general stuff. I don't understand what you mean by a repository. $\endgroup$ – WYSIWYG Jun 21 '15 at 11:06
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Prosite (http://prosite.expasy.org/) uses regular expressions to search for protein domains, in contrast with Pfam. If you look at an entry, such as http://prosite.expasy.org/cgi-bin/prosite/prosite-search-ac?PDOC00022, you can see the consensus pattern under the PATTERN section towards the bottom. Prosite does not have the same coverage as Pfam, but the ease of searching means it is updated much more frequently and has tighter integration with UniProt.

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Regular expressions are not commonly used for DNA or Protein analysis, but many people use Hidden-Markov-Models (HMMs).

If you are looking at protein domains, you can find many HMMs here: http://pfam.xfam.org/

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You will probably want to read up on Position Frequency Matrices (PFMs) and Position Weight Matrices (PWMs). These tend to be much more sensitive and useful for pattern recognition in nuclei acid sequences. Two examples of databases with these patterns are TRANSFAC and JASPAR. Regex patterns can be useful in protein sequences sometimes, although PWM have application there as well.

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